FAM124A

family with sequence similarity 124 member A

Basic information

Region (hg38): 13:51222334-51284239

Links

ENSG00000150510 ∙ NCBI:220108 ∙ ∙ HGNC:26413 ∙ Uniprot:Q86V42 ∙ 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 FAM124A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM124A 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					2	2
missense			34		1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	34	0	3

Variants in FAM124A

This is a list of pathogenic ClinVar variants found in the FAM124A region.

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

Position	Type	Phenotype	Significance	ClinVar
13-51222513-G-T		not specified	Uncertain significance (Sep 13, 2023)
13-51222521-G-T		not specified	Uncertain significance (Aug 08, 2022)
13-51231352-G-A		not specified	Uncertain significance (Oct 07, 2024)
13-51231362-A-C		not specified	Uncertain significance (Apr 13, 2022)
13-51251465-C-T			Benign (Oct 27, 2017)
13-51251492-A-G		not specified	Uncertain significance (Sep 14, 2022)
13-51251497-C-A		not specified	Uncertain significance (Nov 01, 2021)
13-51251545-C-A		not specified	Uncertain significance (Nov 12, 2021)
13-51251575-G-A		not specified	Uncertain significance (Oct 05, 2023)
13-51251598-G-A			Benign (Nov 16, 2017)
13-51251630-G-A		not specified	Uncertain significance (Nov 14, 2024)
13-51251639-G-A		not specified	Uncertain significance (Jun 19, 2024)
13-51251694-G-C		not specified	Uncertain significance (Jan 04, 2024)
13-51251696-A-T		not specified	Uncertain significance (Jul 12, 2022)
13-51251735-T-C		not specified	Uncertain significance (Mar 02, 2023)
13-51251767-G-A		not specified	Uncertain significance (Apr 25, 2023)
13-51251827-G-A		not specified	Uncertain significance (Feb 28, 2024)
13-51251884-C-A		not specified	Uncertain significance (Jun 10, 2022)
13-51251902-C-T		not specified	Uncertain significance (Nov 25, 2024)
13-51251903-G-T		not specified	Uncertain significance (Nov 12, 2021)
13-51251923-A-G		not specified	Uncertain significance (Sep 14, 2022)
13-51251950-C-T		not specified	Uncertain significance (Dec 07, 2024)
13-51251957-G-T		not specified	Uncertain significance (Apr 17, 2023)
13-51251968-A-C		not specified	Uncertain significance (Oct 07, 2024)
13-51252010-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM124A	protein_coding	protein_coding	ENST00000280057	5	61875

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.59e-10	0.110	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.993	292	344	0.849	0.0000215	3753
Missense in Polyphen		105	139.1	0.75484		1497
Synonymous	1.30	133	154	0.866	0.0000102	1219
Loss of Function	0.252	15	16.1	0.932	8.75e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000980	0.000979
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000980	0.000979
South Asian	0.000429	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.373
• hipred: N
• hipred_score: 0.153
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam124a

Gene ontology

• Molecular function: protein binding