FAM47B

family with sequence similarity 47 member B

Basic information

Region (hg38): X:34942796-34944915

Links

ENSG00000189132 ∙ NCBI:170062 ∙ ∙ HGNC:26659 ∙ Uniprot:Q8NA70 ∙ 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 FAM47B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM47B 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			49	5		54
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	50	7	0

Variants in FAM47B

This is a list of pathogenic ClinVar variants found in the FAM47B 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-34942838-G-A		not specified	Uncertain significance (Jul 19, 2023)
X-34942842-G-A		not specified	Likely benign (Jul 13, 2022)
X-34942849-A-G		FAM47B-related disorder	Likely benign (Jul 31, 2019)
X-34942861-A-C		FAM47B-related disorder	Likely benign (Jul 31, 2019)
X-34942870-A-G		FAM47B-related disorder	Likely benign (Jul 31, 2019)
X-34942880-T-A		not specified	Uncertain significance (May 30, 2024)
X-34942922-G-T		not specified	Uncertain significance (Jan 30, 2024)
X-34942928-C-T		not specified	Uncertain significance (Jan 31, 2025)
X-34942940-C-A		not specified	Uncertain significance (Nov 21, 2022)
X-34942944-T-C		not specified	Uncertain significance (Jan 20, 2025)
X-34943007-G-A		not specified	Uncertain significance (Dec 26, 2024)
X-34943021-T-C		not specified	Uncertain significance (Apr 07, 2022)
X-34943057-T-C		not specified	Uncertain significance (Mar 31, 2022)
X-34943094-C-T		not specified	Uncertain significance (Dec 05, 2024)
X-34943154-CGCCAGTACA-C		FAM47B-related disorder	Likely benign (May 27, 2022)
X-34943160-T-C		not specified	Likely benign (Sep 14, 2022)
X-34943226-C-T		not specified	Uncertain significance (Oct 29, 2024)
X-34943277-T-C		not specified	Uncertain significance (May 28, 2023)
X-34943337-G-A		not specified	Likely benign (Dec 05, 2022)
X-34943351-G-A		not specified	Uncertain significance (Oct 22, 2021)
X-34943403-CTCCCGAGACTCCGGTGTCCCGTCTCCGTCCTCAGCT-C			Uncertain significance (Sep 03, 2021)
X-34943408-G-A		not specified	Uncertain significance (Dec 18, 2023)
X-34943416-G-A			Likely benign (Nov 01, 2022)
X-34943430-G-A		not specified	Uncertain significance (Dec 21, 2022)
X-34943450-C-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM47B	protein_coding	protein_coding	ENST00000329357	1	2122

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	-0.714	348	312	1.11	0.0000292	4180
Missense in Polyphen		89	74.118	1.2008		1301
Synonymous	-1.46	146	125	1.17	0.0000120	1354
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: 0.700
• rvis_EVS: 1.87
• rvis_percentile_EVS: 97.2

Haploinsufficiency Scores

• pHI: 0.0372
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00399

Gene Damage Prediction

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