NM_001378454.1(ALMS1):c.11963T>C (p.Phe3988Ser) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 31, 2023
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:: RCV002338567.3

Allele description [Variation Report for NM_001378454.1(ALMS1):c.11963T>C (p.Phe3988Ser)]

NM_001378454.1(ALMS1):c.11963T>C (p.Phe3988Ser)

Genes:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
LOC126806252:BRD4-independent group 4 enhancer GRCh37_chr2:73828496-73829695 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_001378454.1(ALMS1):c.11963T>C (p.Phe3988Ser)

HGVS:

NC_000002.12:g.73601285T>C
NG_011690.1:g.220533T>C
NG_082576.1:g.17T>C
NM_001378454.1:c.11963T>CMANE SELECT
NM_015120.4:c.11966T>C
NP_001365383.1:p.Phe3988Ser
NP_055935.3:p.Phe3989Ser
NP_055935.4:p.Phe3989Ser
LRG_741t1:c.11966T>C
LRG_741:g.220533T>C
LRG_741p1:p.Phe3989Ser
NC_000002.11:g.73828412T>C
NM_015120.3:c.11966T>C

Protein change:

F3988S

Molecular consequence:

NM_001378454.1:c.11963T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015120.4:c.11966T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002643785	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 31, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002643785

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 31, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002643785.3

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

Description

The p.F3989S variant (also known as c.11966T>C), located in coding exon 19 of the ALMS1 gene, results from a T to C substitution at nucleotide position 11966. The phenylalanine at codon 3989 is replaced by serine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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