FAM47A

family with sequence similarity 47 member A

Basic information

Region (hg38): X:34129752-34132314

Links

ENSG00000185448 ∙ NCBI:158724 ∙ ∙ HGNC:29962 ∙ Uniprot:Q5JRC9 ∙ 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 FAM47A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM47A 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				4		4
missense			57	7	1	65
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	11	2

Variants in FAM47A

This is a list of pathogenic ClinVar variants found in the FAM47A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-34129910-T-C		not specified	Uncertain significance (Nov 08, 2022)
X-34129910-T-G		not specified	Uncertain significance (Sep 29, 2023)
X-34129923-C-T			Likely benign (Sep 01, 2024)
X-34129926-C-T		not specified	Uncertain significance (Feb 07, 2025)
X-34130018-A-G		not specified	Uncertain significance (May 21, 2024)
X-34130022-T-A		not specified	Uncertain significance (Feb 16, 2023)
X-34130028-G-C		not specified	Uncertain significance (Jun 11, 2021)
X-34130040-C-T		not specified	Uncertain significance (Dec 31, 2024)
X-34130060-T-G		not specified	Uncertain significance (Nov 29, 2024)
X-34130083-A-G			Likely benign (Jan 01, 2023)
X-34130087-T-C		not specified	Uncertain significance (Oct 12, 2022)
X-34130094-C-T		not specified	Likely benign (Feb 08, 2025)
X-34130214-G-C		not specified	Uncertain significance (Dec 11, 2023)
X-34130242-G-C		not specified	Uncertain significance (Jun 07, 2024)
X-34130309-C-G		not specified	Uncertain significance (Aug 12, 2021)
X-34130324-G-A		not specified	Uncertain significance (Sep 20, 2024)
X-34130361-C-T		not specified	Uncertain significance (Jan 24, 2023)
X-34130381-G-A		not specified	Uncertain significance (Jul 19, 2022)
X-34130553-G-C		FAM47A-related disorder	Benign (May 31, 2019)
X-34130572-G-T		Intellectual disability • not specified	Uncertain significance (Aug 28, 2024)
X-34130599-A-G		FAM47A-related disorder	Likely benign (Apr 01, 2022)
X-34130607-G-A		not specified	Uncertain significance (Dec 08, 2023)
X-34130622-C-T		not specified	Uncertain significance (Aug 11, 2022)
X-34130625-G-A		not specified	Uncertain significance (Dec 04, 2024)
X-34130628-G-A		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM47A	protein_coding	protein_coding	ENST00000346193	1	2579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0791	366	370	0.988	0.0000347	5104
Missense in Polyphen		156	168.32	0.92682		2626
Synonymous	-0.787	163	151	1.08	0.0000142	1677
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.515
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.24

Haploinsufficiency Scores

• pHI: 0.0290
• hipred: N
• hipred_score: 0.293

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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