NM_001844.5(COL2A1):c.4103C>T (p.Pro1368Leu) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001536928.8

Allele description [Variation Report for NM_001844.5(COL2A1):c.4103C>T (p.Pro1368Leu)]

NM_001844.5(COL2A1):c.4103C>T (p.Pro1368Leu)

Gene:

COL2A1:collagen type II alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_001844.5(COL2A1):c.4103C>T (p.Pro1368Leu)

HGVS:

NC_000012.12:g.47974303G>A
NG_008072.1:g.35200C>T
NM_001844.5:c.4103C>TMANE SELECT
NM_033150.3:c.3896C>T
NP_001835.3:p.Pro1368Leu
NP_149162.2:p.Pro1299Leu
NC_000012.11:g.48368086G>A
NM_001844.4:c.4103C>T

Protein change:

P1299L

Links:

dbSNP: rs149375186

NCBI 1000 Genomes Browser:

rs149375186

Molecular consequence:

NM_001844.5:c.4103C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033150.3:c.3896C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens retrotransposon Gag like 9 (RTL9), transcript variant X5...
PREDICTED: Homo sapiens retrotransposon Gag like 9 (RTL9), transcript variant X5, mRNA
gi|2462630282|ref|XM_054327459.1|

Nucleotide
Homo sapiens ubiquitin protein ligase E3 component n-recognin 3 (UBR3), mRNA
Homo sapiens ubiquitin protein ligase E3 component n-recognin 3 (UBR3), mRNA
gi|1720076830|ref|NM_172070.4|

Nucleotide
SRX23430884 (1)
SRA
Acrocephalus hiwae isolate M68 cytochrome b (cytb) gene, partial cds; mitochondr...
Acrocephalus hiwae isolate M68 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2196326235|gb|OM221379.1|

Nucleotide
Acrocephalus yamashinae isolate UA4 cytochrome b (cytb) gene, partial cds; mitoc...
Acrocephalus yamashinae isolate UA4 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2196326249|gb|OM221386.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001753744	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jan 22, 2019)	germline	clinical testing	Citation Link,
SCV002313796	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001753744

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jan 22, 2019)

germline

clinical testing

Citation Link,

SCV002313796

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 27, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From GeneDx, SCV001753744.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002313796.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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