FAM43A

family with sequence similarity 43 member A

Basic information

Region (hg38): 3:194685882-194689037

Links

ENSG00000185112 ∙ NCBI:131583 ∙ ∙ HGNC:26888 ∙ Uniprot:Q8N2R8 ∙ 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 FAM43A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM43A 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			24	1	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	2

Variants in FAM43A

This is a list of pathogenic ClinVar variants found in the FAM43A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194686866-G-C		not specified	Uncertain significance (Dec 28, 2022)
3-194686878-C-G		not specified	Uncertain significance (Dec 13, 2023)
3-194686942-C-T		not specified	Uncertain significance (Nov 09, 2023)
3-194686958-A-T		not specified	Uncertain significance (Nov 12, 2021)
3-194686962-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-194687005-A-C		not specified	Uncertain significance (Oct 25, 2022)
3-194687031-A-G		not specified	Uncertain significance (Mar 30, 2024)
3-194687085-G-A		not specified	Uncertain significance (Aug 08, 2022)
3-194687163-G-A		not specified	Uncertain significance (Mar 28, 2024)
3-194687221-G-C		not specified	Uncertain significance (Mar 16, 2024)
3-194687256-G-C		not specified	Uncertain significance (Aug 30, 2022)
3-194687380-C-T		not specified	Uncertain significance (Jan 02, 2024)
3-194687407-A-G		not specified	Uncertain significance (Aug 29, 2023)
3-194687544-C-T		not specified	Uncertain significance (Mar 11, 2022)
3-194687573-G-T			Benign (Dec 27, 2017)
3-194687583-A-C		not specified	Uncertain significance (Feb 17, 2024)
3-194687640-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-194687668-A-T		not specified	Uncertain significance (Dec 19, 2023)
3-194687680-G-T		not specified	Uncertain significance (Jan 05, 2022)
3-194687706-G-C		not specified	Uncertain significance (Aug 15, 2023)
3-194687715-G-A			Benign (Dec 27, 2017)
3-194687802-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-194687809-G-A			Likely benign (Nov 01, 2022)
3-194687823-G-C		not specified	Uncertain significance (May 31, 2023)
3-194687833-C-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM43A	protein_coding	protein_coding	ENST00000329759	1	3141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.408	0.585	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	157	219	0.716	0.0000100	2641
Missense in Polyphen		65	104.97	0.61921		1182
Synonymous	-0.340	105	101	1.04	0.00000483	898
Loss of Function	2.24	2	9.40	0.213	4.02e-7	117

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.458
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam43a