FAM72A

family with sequence similarity 72 member A

Basic information

Region (hg38): 1:206186179-206204414

Links

ENSG00000196550 ∙ NCBI:729533 ∙ OMIM:614710 ∙ HGNC:24044 ∙ Uniprot:Q5TYM5 ∙ 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 FAM72A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM72A 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in FAM72A

This is a list of pathogenic ClinVar variants found in the FAM72A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-206195869-T-C		not specified	Uncertain significance (Oct 01, 2024)
1-206199826-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-206199852-G-C		not specified	Uncertain significance (Dec 19, 2022)
1-206199880-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-206201908-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-206201968-A-C		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM72A	protein_coding	protein_coding	ENST00000367128	4	18236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0328	0.628	124571	0	5	124576	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.818	26	40.7	0.639	0.00000197	990
Missense in Polyphen		8	16.198	0.4939		387
Synonymous	0.0910	14	14.4	0.970	8.20e-7	261
Loss of Function	0.282	2	2.48	0.807	1.04e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000888	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.000140	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of cellular reactive oxygen species metabolism. May participate in cell growth regulation. {ECO:0000269|PubMed:21317926}.

Haploinsufficiency Scores

• pHI: 0.619
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Fam72a

Gene ontology

• Cellular component: mitochondrion;cytosol;membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding