NM_174878.3(CLRN1):c.322C>T (p.Leu108Phe) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 5, 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:: RCV002541728.1

Allele description

NM_174878.3(CLRN1):c.322C>T (p.Leu108Phe)

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.322C>T (p.Leu108Phe)

HGVS:

NC_000003.12:g.150941693G>A
NG_009168.1:g.36307C>T
NM_001195794.1:c.322C>T
NM_001256819.2:c.494C>T
NM_052995.2:c.94C>T
NM_174878.3:c.322C>TMANE SELECT
NP_001182723.1:p.Leu108Phe
NP_001243748.1:p.Pro165Leu
NP_443721.1:p.Leu32Phe
NP_777367.1:p.Leu108Phe
LRG_700t1:c.322C>T
LRG_700t2:c.94C>T
LRG_700:g.36307C>T
LRG_700p1:p.Leu108Phe
LRG_700p2:p.Leu32Phe
NC_000003.11:g.150659480G>A
NR_046380.3:n.492C>T

Protein change:

L108F

Links:

dbSNP: rs144691725

NCBI 1000 Genomes Browser:

rs144691725

Molecular consequence:

NM_001195794.1:c.322C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001256819.2:c.494C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_052995.2:c.94C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_174878.3:c.322C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_046380.3:n.492C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention rece...
Homo sapiens KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2, mRNA (cDNA clone MGC:655 IMAGE:2966703), complete cds
gi|33990642|gb|BC008081.2|

Nucleotide
SRSF protein kinase 2 isoform h [Homo sapiens]
SRSF protein kinase 2 isoform h [Homo sapiens]
gi|1184495053|ref|NP_001337674.1|

Protein
RecName: Full=Solute carrier organic anion transporter family member 1C1; AltNam...
RecName: Full=Solute carrier organic anion transporter family member 1C1; AltName: Full=Organic anion transporter 1C1; Short=OATP1C1; AltName: Full=Organic anion transporter F; Short=OATP-F; AltName: Full=Organic anion transporter polypeptide-related protein 5; Short=OAT-RP-5; Short=OATP-RP5; AltName: Full=Organic anion-transporting polypeptide 14; Short=OATP-14; AltName: Full=Solute carrier family 21 member 14; AltName: Full=Thyroxine transporter
gi|27734564|sp|Q9NYB5.1|SO1C1_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003446813	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 5, 2022)	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

SCV003446813

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 5, 2022)

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	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 Invitae, SCV003446813.1

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

Description

This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 108 of the CLRN1 protein (p.Leu108Phe). This variant is present in population databases (rs144691725, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with CLRN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 991770). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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: Dec 24, 2023

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