FAM9B

family with sequence similarity 9 member B

Basic information

Region (hg38): X:9024232-9295682

Links

ENSG00000177138 ∙ NCBI:171483 ∙ OMIM:300478 ∙ HGNC:18404 ∙ Uniprot:Q8IZU0 ∙ 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 FAM9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM9B 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				1		1
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	1	2

Variants in FAM9B

This is a list of pathogenic ClinVar variants found in the FAM9B 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-9025523-C-G		not specified	Uncertain significance (Sep 13, 2023)
X-9025532-T-C		not specified	Uncertain significance (Jun 13, 2024)
X-9025541-C-T		not specified	Uncertain significance (May 14, 2024)
X-9025561-A-C		not specified	Uncertain significance (Oct 03, 2022)
X-9025570-A-T		not specified	Uncertain significance (May 07, 2024)
X-9027858-T-C			Benign (Aug 30, 2018)
X-9027873-C-T		not specified	Uncertain significance (Nov 13, 2023)
X-9027884-C-T		not specified	Uncertain significance (Dec 27, 2023)
X-9027885-G-A		not specified	Uncertain significance (Dec 06, 2023)
X-9027890-A-G		not specified	Uncertain significance (Apr 17, 2024)
X-9029399-G-A			Benign (Jun 20, 2018)
X-9029411-G-A		not specified	Uncertain significance (May 03, 2023)
X-9030267-A-G		not specified	Uncertain significance (Dec 19, 2023)
X-9032136-T-C		not specified	Uncertain significance (Oct 20, 2023)
X-9032159-G-A		not specified	Uncertain significance (Jul 25, 2023)
X-9032458-T-C		not specified	Uncertain significance (Jan 02, 2024)
X-9032981-C-A			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM9B	protein_coding	protein_coding	ENST00000327220	7	140408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000306	0.355	125690	2	22	125714	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.630	81	66.5	1.22	0.00000521	1257
Missense in Polyphen		35	27.513	1.2721		511
Synonymous	0.0114	21	21.1	0.997	0.00000162	281
Loss of Function	0.133	7	7.39	0.947	4.65e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000697	0.000667
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000723	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000868	0.0000615
Middle Eastern	0.0000723	0.0000544
South Asian	0.00	0.00
Other	0.000253	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.481
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.0444
• hipred: N
• hipred_score: 0.112
• ghis: 0.383

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0588

Gene Damage Prediction

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

Gene ontology

• Biological process: spermatogenesis;spermatid development;meiotic cell cycle
• Cellular component: synaptonemal complex;nucleoplasm
• Molecular function: protein binding