ClinVar Genomic variation as it relates to human health
NM_001405607.1(PBRM1):c.4043_4050del (p.Asp1348fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001405607.1(PBRM1):c.4043_4050del (p.Asp1348fs)
Variation ID: 218955 Accession: VCV000218955.4
- Type and length
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Deletion, 8 bp
- Location
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Cytogenetic: 3p21.1 3: 52563364-52563371 (GRCh38) [ NCBI UCSC ] 3: 52597380-52597387 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline May 10, 2018 Jan 6, 2024 Jun 1, 2015 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001405607.1:c.4043_4050del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001392536.1:p.Asp1348fs frameshift NM_001350074.2:c.4106_4113del NP_001337003.1:p.Asp1369fs frameshift NM_001350075.2:c.3998_4005del NP_001337004.1:p.Asp1333fs frameshift NM_001350076.2:c.4103_4110del NP_001337005.1:p.Asp1368fs frameshift NM_001350077.2:c.4097_4104del NP_001337006.1:p.Asp1366fs frameshift NM_001350078.2:c.4106_4113del NP_001337007.1:p.Asp1369fs frameshift NM_001350079.2:c.3986_3993del NP_001337008.1:p.Asp1329fs frameshift NM_001366070.2:c.4106_4113del NP_001352999.1:p.Asp1369fs frameshift NM_001366071.2:c.4061_4068del NP_001353000.1:p.Asp1354fs frameshift NM_001366072.2:c.4061_4068del NP_001353001.1:p.Asp1354fs frameshift NM_001366073.2:c.4052_4059del NP_001353002.1:p.Asp1351fs frameshift NM_001366074.2:c.4049_4056del NP_001353003.1:p.Asp1350fs frameshift NM_001366075.2:c.4031_4038del NP_001353004.1:p.Asp1344fs frameshift NM_001366076.2:c.4001_4008del NP_001353005.1:p.Asp1334fs frameshift NM_001394867.1:c.3998_4005del NP_001381796.1:p.Asp1333fs frameshift NM_001394868.1:c.3998_4005del NP_001381797.1:p.Asp1333fs frameshift NM_001394869.1:c.3998_4005del NP_001381798.1:p.Asp1333fs frameshift NM_001394870.1:c.4052_4059del NP_001381799.1:p.Asp1351fs frameshift NM_001394871.1:c.3998_4005del NP_001381800.1:p.Asp1333fs frameshift NM_001394872.1:c.3998_4005del NP_001381801.1:p.Asp1333fs frameshift NM_001394873.1:c.3995_4002del NP_001381802.1:p.Asp1332fs frameshift NM_001394874.1:c.3995_4002del NP_001381803.1:p.Asp1332fs frameshift NM_001394875.1:c.3998_4005del NP_001381804.1:p.Asp1333fs frameshift NM_001394876.1:c.3995_4002del NP_001381805.1:p.Asp1332fs frameshift NM_001394877.1:c.3995_4002del NP_001381806.1:p.Asp1332fs frameshift NM_001394878.1:c.3962_3969del NP_001381807.1:p.Asp1321fs frameshift NM_001394879.1:c.3902_3909del NP_001381808.1:p.Asp1301fs frameshift NM_001400470.1:c.3998_4005del NP_001387399.1:p.Asp1333fs frameshift NM_001400471.1:c.3968_3975del NP_001387400.1:p.Asp1323fs frameshift NM_001400472.1:c.4019_4026del NP_001387401.1:p.Asp1340fs frameshift NM_001400473.1:c.3995_4002del NP_001387402.1:p.Asp1332fs frameshift NM_001400474.1:c.3998_4005del NP_001387403.1:p.Asp1333fs frameshift NM_001400475.1:c.3998_4005del NP_001387404.1:p.Asp1333fs frameshift NM_001400479.1:c.3998_4005del NP_001387408.1:p.Asp1333fs frameshift NM_001400481.1:c.3995_4002del NP_001387410.1:p.Asp1332fs frameshift NM_001400484.1:c.3923_3930del NP_001387413.1:p.Asp1308fs frameshift NM_001400487.1:c.3902_3909del NP_001387416.1:p.Asp1301fs frameshift NM_001400490.1:c.3923_3930del NP_001387419.1:p.Asp1308fs frameshift NM_001400496.1:c.3998_4005del NP_001387425.1:p.Asp1333fs frameshift NM_001400500.1:c.3998_4005del NP_001387429.1:p.Asp1333fs frameshift NM_001400501.1:c.3998_4005del NP_001387430.1:p.Asp1333fs frameshift NM_001400504.1:c.3923_3930del NP_001387433.1:p.Asp1308fs frameshift NM_001405552.1:c.4100_4107del NP_001392481.1:p.Asp1367fs frameshift NM_001405553.1:c.4061_4068del NP_001392482.1:p.Asp1354fs frameshift NM_001405554.1:c.4103_4110del NP_001392483.1:p.Asp1368fs frameshift NM_001405555.1:c.3998_4005del NP_001392484.1:p.Asp1333fs frameshift NM_001405556.1:c.3998_4005del NP_001392485.1:p.Asp1333fs frameshift NM_001405557.1:c.3998_4005del NP_001392486.1:p.Asp1333fs frameshift NM_001405558.1:c.3923_3930del NP_001392487.1:p.Asp1308fs frameshift NM_001405559.1:c.3923_3930del NP_001392488.1:p.Asp1308fs frameshift NM_001405560.1:c.3899_3906del NP_001392489.1:p.Asp1300fs frameshift NM_001405561.1:c.3995_4002del NP_001392490.1:p.Asp1332fs frameshift NM_001405563.1:c.3995_4002del NP_001392492.1:p.Asp1332fs frameshift NM_001405564.1:c.4025_4032del NP_001392493.1:p.Asp1342fs frameshift NM_001405565.1:c.3923_3930del NP_001392494.1:p.Asp1308fs frameshift NM_001405566.1:c.2090_2097del NP_001392495.1:p.Asp697fs frameshift NM_001405567.1:c.3995_4002del NP_001392496.1:p.Asp1332fs frameshift NM_001405568.1:c.4025_4032del NP_001392497.1:p.Asp1342fs frameshift NM_001405569.1:c.4022_4029del NP_001392498.1:p.Asp1341fs frameshift NM_001405570.1:c.3998_4005del NP_001392499.1:p.Asp1333fs frameshift NM_001405571.1:c.4043_4050del NP_001392500.1:p.Asp1348fs frameshift NM_001405572.1:c.3824_3831del NP_001392501.1:p.Asp1275fs frameshift NM_001405573.1:c.3809_3816del NP_001392502.1:p.Asp1270fs frameshift NM_001405574.1:c.4049_4056del NP_001392503.1:p.Asp1350fs frameshift NM_001405575.1:c.3995_4002del NP_001392504.1:p.Asp1332fs frameshift NM_001405576.1:c.3920_3927del NP_001392505.1:p.Asp1307fs frameshift NM_001405577.1:c.3998_4005del NP_001392506.1:p.Asp1333fs frameshift NM_001405578.1:c.3995_4002del NP_001392507.1:p.Asp1332fs frameshift NM_001405579.1:c.3995_4002del NP_001392508.1:p.Asp1332fs frameshift NM_001405580.1:c.3944_3951del NP_001392509.1:p.Asp1315fs frameshift NM_001405581.1:c.3998_4005del NP_001392510.1:p.Asp1333fs frameshift NM_001405582.1:c.3902_3909del NP_001392511.1:p.Asp1301fs frameshift NM_001405583.1:c.3998_4005del NP_001392512.1:p.Asp1333fs frameshift NM_001405584.1:c.3998_4005del NP_001392513.1:p.Asp1333fs frameshift NM_001405585.1:c.3995_4002del NP_001392514.1:p.Asp1332fs frameshift NM_001405586.1:c.3947_3954del NP_001392515.1:p.Asp1316fs frameshift NM_001405587.1:c.3854_3861del NP_001392516.1:p.Asp1285fs frameshift NM_001405588.1:c.3923_3930del NP_001392517.1:p.Asp1308fs frameshift NM_001405589.1:c.3995_4002del NP_001392518.1:p.Asp1332fs frameshift NM_001405590.1:c.3995_4002del NP_001392519.1:p.Asp1332fs frameshift NM_001405591.1:c.3977_3984del NP_001392520.1:p.Asp1326fs frameshift NM_001405592.1:c.3923_3930del NP_001392521.1:p.Asp1308fs frameshift NM_001405593.1:c.3998_4005del NP_001392522.1:p.Asp1333fs frameshift NM_001405594.1:c.3998_4005del NP_001392523.1:p.Asp1333fs frameshift NM_001405595.1:c.3929_3936del NP_001392524.1:p.Asp1310fs frameshift NM_001405596.1:c.2090_2097del NP_001392525.1:p.Asp697fs frameshift NM_001405597.1:c.3881_3888del NP_001392526.1:p.Asp1294fs frameshift NM_001405598.1:c.4025_4032del NP_001392527.1:p.Asp1342fs frameshift NM_001405599.1:c.3902_3909del NP_001392528.1:p.Asp1301fs frameshift NM_001405600.1:c.4052_4059del NP_001392529.1:p.Asp1351fs frameshift NM_001405601.1:c.4043_4050del NP_001392530.1:p.Asp1348fs frameshift NM_001405602.1:c.3899_3906del NP_001392531.1:p.Asp1300fs frameshift NM_001405603.1:c.3998_4005del NP_001392532.1:p.Asp1333fs frameshift NM_001405604.1:c.3902_3909del NP_001392533.1:p.Asp1301fs frameshift NM_001405605.1:c.3923_3930del NP_001392534.1:p.Asp1308fs frameshift NM_001405606.1:c.3902_3909del NP_001392535.1:p.Asp1301fs frameshift NM_001405608.1:c.2786_2793del NP_001392537.1:p.Asp929fs frameshift NM_001405609.1:c.3998_4005del NP_001392538.1:p.Asp1333fs frameshift NM_001405610.1:c.3998_4005del NP_001392539.1:p.Asp1333fs frameshift NM_001405611.1:c.3920_3927del NP_001392540.1:p.Asp1307fs frameshift NM_001405622.1:c.4061_4068del NP_001392551.1:p.Asp1354fs frameshift NM_001405623.1:c.3998_4005del NP_001392552.1:p.Asp1333fs frameshift NM_001405624.1:c.3995_4002del NP_001392553.1:p.Asp1332fs frameshift NM_001405625.1:c.2357_2364del NP_001392554.1:p.Asp786fs frameshift NM_001405626.1:c.3998_4005del NP_001392555.1:p.Asp1333fs frameshift NM_001405627.1:c.3998_4005del NP_001392556.1:p.Asp1333fs frameshift NM_001405628.1:c.3998_4005del NP_001392557.1:p.Asp1333fs frameshift NM_001405629.1:c.3995_4002del NP_001392558.1:p.Asp1332fs frameshift NM_001405630.1:c.3998_4005del NP_001392559.1:p.Asp1333fs frameshift NM_001405631.1:c.3998_4005del NP_001392560.1:p.Asp1333fs frameshift NM_001405632.1:c.3995_4002del NP_001392561.1:p.Asp1332fs frameshift NM_001405633.1:c.3923_3930del NP_001392562.1:p.Asp1308fs frameshift NM_001405634.1:c.3923_3930del NP_001392563.1:p.Asp1308fs frameshift NM_001405635.1:c.3923_3930del NP_001392564.1:p.Asp1308fs frameshift NM_001405636.1:c.4025_4032del NP_001392565.1:p.Asp1342fs frameshift NM_001405637.1:c.4016_4023del NP_001392566.1:p.Asp1339fs frameshift NM_001405638.1:c.3902_3909del NP_001392567.1:p.Asp1301fs frameshift NM_001405639.1:c.3923_3930del NP_001392568.1:p.Asp1308fs frameshift NM_001405640.1:c.3998_4005del NP_001392569.1:p.Asp1333fs frameshift NM_001405641.1:c.3998_4005del NP_001392570.1:p.Asp1333fs frameshift NM_001405642.1:c.3899_3906del NP_001392571.1:p.Asp1300fs frameshift NM_001405643.1:c.3998_4005del NP_001392572.1:p.Asp1333fs frameshift NM_018165.4:c.3900_3907delAGATAGTG NP_060635.2:p.Asp1301Glyfs frameshift NM_018313.5:c.3923_3930del NP_060783.3:p.Asp1308fs frameshift NM_181042.5:c.3998_4005del NP_851385.1:p.Asp1333fs frameshift NR_174502.1:n.4178_4185del non-coding transcript variant NR_175959.1:n.4220_4227del non-coding transcript variant NC_000003.12:g.52563366_52563373del NC_000003.11:g.52597382_52597389del NG_032108.1:g.127480_127487del - Protein change
- D1344fs, D1351fs, D1329fs, D1334fs, D1366fs, D1308fs, D1333fs, D1350fs, D1368fs, D1369fs, D1354fs, D1270fs, D1275fs, D1285fs, D1294fs, D1300fs, D1301fs, D1307fs, D1310fs, D1315fs, D1316fs, D1321fs, D1323fs, D1326fs, D1332fs, D1339fs, D1340fs, D1341fs, D1342fs, D1348fs, D1367fs, D697fs, D786fs, D929fs
- Other names
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- Canonical SPDI
- NC_000003.12:52563363:CTCACTATCT:CT
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
- Comment on variant
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| PBRM1 | - | - |
GRCh38 GRCh37 |
65 | 76 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
no assertion criteria provided
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Jun 1, 2015 | RCV000203297.5 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jun 01, 2015)
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no assertion criteria provided
Method: literature only
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RENAL CELL CARCINOMA, CLEAR CELL (1 family)
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000258424.5
First in ClinVar: Jan 10, 2016 Last updated: Jan 06, 2024 |
Comment on evidence:
In a family with clear cell renal cell carcinoma (ccRCC; 144700) in 3 generations, Benusiglio et al. (2015) identified a heterozygous germline mutation in PBRM1, … (more)
In a family with clear cell renal cell carcinoma (ccRCC; 144700) in 3 generations, Benusiglio et al. (2015) identified a heterozygous germline mutation in PBRM1, an 8-bp deletion (c.3998_4005del, ENST00000296302) in exon 24 that resulted in an asp-to-gly substitution at codon 1333 with a frameshift 3 amino acids downstream (Asp1333Glyfs). Neither this mutation nor any PBRM1 truncating mutation was reported in 6,503 Caucasian and African American individuals in the NHLBI Exome Sequencing Project Exome Variant Server. The mutation segregated with the disease in the family that included the proband, who was diagnosed at age 38; his older sister, diagnosed at age 42; that sister's daughter, diagnosed at age 36; and the mother of the proband, who was diagnosed at ages 64 and 70 with clear cell renal cell carcinoma. (less)
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Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| A germline mutation in PBRM1 predisposes to renal cell carcinoma. | Benusiglio PR | Journal of medical genetics | 2015 | PMID: 25911086 |
Text-mined citations for rs864321679 ...
HelpRecord last updated Jan 06, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
NCBI staff reviewed the sequence information reported in PubMed 25911086 Fig. 2 to determine the location of this allele on the current reference sequence.