VCV002678001.1 - ClinVar

NM_001077365.2(POMT1):c.1477_1486del (p.Tyr493fs)

Germline

Classification

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.

(1)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001077365.2(POMT1):c.1477_1486del (p.Tyr493fs)

Variation ID: 2678001 Accession: VCV002678001.1

Type and length

Deletion, 10 bp

Location

Cytogenetic: 9q34.13 9: 131518945-131518954 (GRCh38) [ NCBI UCSC ] 9: 134394332-134394341 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Dec 30, 2023	Dec 30, 2023	Sep 3, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001077365.2:c.1477_1486del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001070833.1:p.Tyr493fs	frameshift
NM_001077366.2:c.1315_1324del	NP_001070834.1:p.Tyr439fs	frameshift
NM_001136113.2:c.1477_1486del	NP_001129585.1:p.Tyr493fs	frameshift
NM_001136114.2:c.1126_1135del	NP_001129586.1:p.Tyr376fs	frameshift
NM_001353193.2:c.1543_1552del	NP_001340122.2:p.Tyr515fs	frameshift
NM_001353194.2:c.1315_1324del	NP_001340123.1:p.Tyr439fs	frameshift
NM_001353195.2:c.1126_1135del	NP_001340124.1:p.Tyr376fs	frameshift
NM_001353196.2:c.1387_1396del	NP_001340125.1:p.Tyr463fs	frameshift
NM_001353197.2:c.1381_1390del	NP_001340126.2:p.Tyr461fs	frameshift
NM_001353198.2:c.1381_1390del	NP_001340127.2:p.Tyr461fs	frameshift
NM_001353199.2:c.1192_1201del	NP_001340128.2:p.Tyr398fs	frameshift
NM_001353200.2:c.1021_1030del	NP_001340129.1:p.Tyr341fs	frameshift
NM_001374689.1:c.1465_1474del	NP_001361618.1:p.Tyr489fs	frameshift
NM_001374690.1:c.1365+411_1365+420del		intron variant
NM_001374691.1:c.1126_1135del	NP_001361620.1:p.Tyr376fs	frameshift
NM_001374692.1:c.1126_1135del	NP_001361621.1:p.Tyr376fs	frameshift
NM_001374693.1:c.1126_1135del	NP_001361622.1:p.Tyr376fs	frameshift
NM_001374695.1:c.1087_1096del	NP_001361624.1:p.Tyr363fs	frameshift
NM_001411024.1:c.346_355del	NP_001397953.1:p.Tyr116fs	frameshift
NM_007171.4:c.1543_1552del	NP_009102.4:p.Tyr515fs	frameshift
NR_148391.2:n.1511_1520del		non-coding transcript variant
NR_148392.2:n.1729_1738del		non-coding transcript variant
NR_148393.2:n.1650_1659del		non-coding transcript variant
NR_148394.2:n.1404_1413del		non-coding transcript variant
NR_148395.2:n.1802_1811del		non-coding transcript variant
NR_148396.2:n.1436_1445del		non-coding transcript variant
NR_148397.2:n.1561_1570del		non-coding transcript variant
NR_148398.2:n.1516_1525del		non-coding transcript variant
NR_148399.2:n.2042_2051del		non-coding transcript variant
NR_148400.2:n.1641_1650del		non-coding transcript variant
NC_000009.12:g.131518948_131518957del
NC_000009.11:g.134394335_134394344del
NG_008896.2:g.21047_21056del
LRG_842:g.21047_21056del
LRG_842t1:c.1543_1552del	LRG_842p1:p.Tyr515fs
LRG_842t2:c.1477_1486del	LRG_842p2:p.Tyr493fs

... more HGVS ... less HGVS

Protein change

Y116fs, Y341fs, Y363fs, Y376fs, Y398fs, Y439fs, Y461fs, Y463fs, Y489fs, Y493fs, Y515fs

Other names

Canonical SPDI

NC_000009.12:131518944:CGATACGGCGCGA:CGA

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	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.
POMT1		-	-	GRCh38 GRCh37	1160	1201

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 Help 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 Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1	Pathogenic (1)	criteria provided, single submitter	Sep 3, 2023	RCV003471734.1

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 Help 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.
Pathogenic (Sep 03, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004206055.1 First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Mar 30, 2024

ClinVar Genomic variation as it relates to human health

NM_001077365.2(POMT1):c.1477_1486del (p.Tyr493fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...