FAM162A

family with sequence similarity 162 member A

Basic information

Region (hg38): 3:122384161-122412334

Previous symbols: [ "C3orf28" ]

Links

ENSG00000114023 ∙ NCBI:26355 ∙ OMIM:608017 ∙ HGNC:17865 ∙ Uniprot:Q96A26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM162A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM162A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in FAM162A

This is a list of pathogenic ClinVar variants found in the FAM162A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-122384276-T-G		not specified	Uncertain significance (Dec 19, 2022)
3-122402870-G-A		not specified	Likely benign (Mar 11, 2024)
3-122404326-C-T		not specified	Uncertain significance (Mar 29, 2024)
3-122404332-A-G		not specified	Uncertain significance (Sep 14, 2022)
3-122407305-G-C		not specified	Uncertain significance (Dec 03, 2021)
3-122407316-G-A		not specified	Uncertain significance (May 23, 2023)
3-122407333-C-G		not specified	Likely benign (Aug 13, 2021)
3-122407376-T-C		not specified	Uncertain significance (Jan 31, 2022)
3-122409742-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-122409788-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-122409791-G-A		not specified	Uncertain significance (Nov 22, 2023)
3-122409821-A-G		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM162A	protein_coding	protein_coding	ENST00000477892	5	28159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000324	0.352	124608	1	179	124788	0.000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.599	68	83.4	0.815	0.00000432	996
Missense in Polyphen		18	21.606	0.8331		266
Synonymous	0.782	23	28.3	0.813	0.00000156	276
Loss of Function	0.357	9	10.2	0.879	6.97e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000321
Ashkenazi Jewish	0.0145	0.0138
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000203
Middle Eastern	0.0000556	0.0000556
South Asian	0.000102	0.0000980
Other	0.00147	0.00132

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed to be involved in regulation of apoptosis; the exact mechanism may differ between cell types/tissues. May be involved in hypoxia-induced cell death of transformed cells implicating cytochrome C release and caspase activation (such as CASP9) and inducing mitochondrial permeability transition. May be involved in hypoxia-induced cell death of neuronal cells probably by promoting release of AIFM1 from mitochondria to cytoplasm and its translocation to the nucleus; however, the involvement of caspases has been reported conflictingly. {ECO:0000269|PubMed:15082785}.

Recessive Scores

• pRec: 0.0640

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.0631
• hipred: N
• hipred_score: 0.144
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0846

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fam162a

Gene ontology

• Biological process: activation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of apoptotic process;neuron apoptotic process;cellular response to hypoxia;positive regulation of release of cytochrome c from mitochondria
• Cellular component: mitochondrion;cytosol;integral component of membrane
• Molecular function: protein binding