FAM24A

family with sequence similarity 24 member A

Basic information

Region (hg38): 10:122910610-122913111

Links

ENSG00000203795 ∙ NCBI:118670 ∙ ∙ HGNC:23470 ∙ Uniprot:A6NFZ4 ∙ 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 FAM24A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM24A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in FAM24A

This is a list of pathogenic ClinVar variants found in the FAM24A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-122911657-G-A		not specified	Uncertain significance (Dec 13, 2023)
10-122911674-G-A		not specified	Uncertain significance (Oct 06, 2021)
10-122911706-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-122912800-A-T		not specified	Uncertain significance (Feb 05, 2024)
10-122912803-A-G		not specified	Uncertain significance (May 12, 2024)
10-122912813-G-T		not specified	Uncertain significance (Nov 10, 2022)
10-122912827-C-T		not specified	Uncertain significance (Nov 14, 2024)
10-122912926-G-T		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM24A	protein_coding	protein_coding	ENST00000368894	2	2411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0152	0.473	125588	0	2	125590	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	55	60.3	0.912	0.00000311	698
Missense in Polyphen		15	13.44	1.1161		164
Synonymous	0.106	23	23.7	0.972	0.00000143	198
Loss of Function	-0.695	2	1.18	1.69	4.92e-8	17

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.505
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.0457
• hipred: N
• hipred_score: 0.112
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.303

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam24a

Gene ontology

• Cellular component: extracellular region