NM_001201543.2(FAM161A):c.1309A>T (p.Arg437Ter) AND not provided

Germline classification:: Pathogenic (8 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV000153226.46

Allele description [Variation Report for NM_001201543.2(FAM161A):c.1309A>T (p.Arg437Ter)]

NM_001201543.2(FAM161A):c.1309A>T (p.Arg437Ter)

Gene:

FAM161A:FAM161 centrosomal protein A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p15

Genomic location:

Preferred name:

NM_001201543.2(FAM161A):c.1309A>T (p.Arg437Ter)

HGVS:

NC_000002.12:g.61839695T>A
NG_028125.1:g.19449A>T
NM_001201543.2:c.1309A>TMANE SELECT
NM_032180.3:c.1309A>T
NP_001188472.1:p.Arg437Ter
NP_115556.2:p.Arg437Ter
NC_000002.11:g.62066830T>A
NM_001201543.1:c.1309A>T
NM_032180.2:c.1309A>T
NP_115556.2:p.Arg437*
NR_037710.2:n.1272A>T

Protein change:

R437*; ARG437TER

Links:

OMIM: 613596.0002; dbSNP: rs200691042

NCBI 1000 Genomes Browser:

rs200691042

Molecular consequence:

NR_037710.2:n.1272A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001201543.2:c.1309A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_032180.3:c.1309A>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Gm39426 AND (alive[prop]) (1)
Gene
benzyl alcohol O-benzoyltransferase-like [Benincasa hispida]
benzyl alcohol O-benzoyltransferase-like [Benincasa hispida]
gi|1955822941|ref|XP_038900507.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000229237	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Aug 15, 2016)	germline	clinical testing	Citation Link,
SCV000329583	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 9, 2022)	germline	clinical testing	Citation Link,
SCV000943915	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 31, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 20705279, 24651477, 20705278, 26113502, 26574802, 28492532
SCV001246771	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Sep 1, 2023)	germline	clinical testing	Citation Link,
SCV001905556	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001923391	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001953139	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001974089	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	4	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Homozygosity mapping reveals null mutations in FAM161A as a cause of autosomal-recessive retinitis pigmentosa.

Bandah-Rozenfeld D, Mizrahi-Meissonnier L, Farhy C, Obolensky A, Chowers I, Pe'er J, Merin S, Ben-Yosef T, Ashery-Padan R, Banin E, Sharon D.

Am J Hum Genet. 2010 Sep 10;87(3):382-91. doi: 10.1016/j.ajhg.2010.07.022. Epub 2010 Aug 12.

PubMed [citation]

PMID:: 20705279
PMCID:: PMC2933343

Molecular genetics of FAM161A in North American patients with early-onset retinitis pigmentosa.

Venturini G, Di Gioia SA, Harper S, Weigel-DiFranco C, Rivolta C, Berson EL.

PLoS One. 2014;9(3):e92479. doi: 10.1371/journal.pone.0092479.

PubMed [citation]

PMID:: 24651477
PMCID:: PMC3961368

See all PubMed Citations (7)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000229237.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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	unknown	not provided	not provided	not provided		3	not provided	not provided	not provided

From GeneDx, SCV000329583.8

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30718709, 25097241, 25525159, 20705278, 28559085, 26113502, 26574802, 25999674, 31589614, 34426522, 33576794)

#	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, SCV000943915.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Arg437*) in the FAM161A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FAM161A are known to be pathogenic (PMID: 20705278, 20705279, 24651477). This variant is present in population databases (rs200691042, gnomAD 0.05%). This premature translational stop signal has been observed in individuals with FAM161A-related conditions (PMID: 20705278, 26113502, 26574802). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36). For these reasons, this variant has been classified as Pathogenic.

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001246771.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

FAM161A: PM3:Very Strong, PVS1, PM2

#	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		4	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001905556.1

#	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	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001923391.1

#	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001953139.1

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001974089.1

#	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

Last Updated: Nov 10, 2024

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