NM_174878.3(CLRN1):c.407G>A (p.Gly136Glu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 17, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001246418.9

Allele description [Variation Report for NM_174878.3(CLRN1):c.407G>A (p.Gly136Glu)]

NM_174878.3(CLRN1):c.407G>A (p.Gly136Glu)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.407G>A (p.Gly136Glu)

HGVS:

NC_000003.12:g.150941608C>T
NG_009168.1:g.36392G>A
NM_001195794.1:c.407G>A
NM_001256819.2:c.*21G>A
NM_052995.2:c.179G>A
NM_174878.3:c.407G>AMANE SELECT
NP_001182723.1:p.Gly136Glu
NP_443721.1:p.Gly60Glu
NP_777367.1:p.Gly136Glu
LRG_700t1:c.407G>A
LRG_700t2:c.179G>A
LRG_700:g.36392G>A
LRG_700p1:p.Gly136Glu
LRG_700p2:p.Gly60Glu
NC_000003.11:g.150659395C>T
NM_001195794.1:c.407G>A
NM_174878.2:c.407G>A
NR_046380.3:n.577G>A

Protein change:

G136E

Links:

dbSNP: rs779258184

NCBI 1000 Genomes Browser:

rs779258184

Molecular consequence:

NM_001256819.2:c.*21G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001195794.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_052995.2:c.179G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_174878.3:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046380.3:n.577G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001419772	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31960602, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001419772

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Application of targeted panel sequencing and whole exome sequencing for 76 Chinese families with retinitis pigmentosa.

Dan H, Huang X, Xing Y, Shen Y.

Mol Genet Genomic Med. 2020 Mar;8(3):e1131. doi: 10.1002/mgg3.1131. Epub 2020 Jan 20.

PubMed [citation]

PMID:: 31960602
PMCID:: PMC7057118

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 Invitae, SCV001419772.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 136 of the CLRN1 protein (p.Gly136Glu). This variant is present in population databases (rs779258184, gnomAD 0.2%). This missense change has been observed in individual(s) with clinical features of CLRN1-related conditions (PMID: 31960602). ClinVar contains an entry for this variant (Variation ID: 556027). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Jun 29, 2024

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