FAM9A

family with sequence similarity 9 member A

Basic information

Region (hg38): X:8790795-8801383

Links

ENSG00000183304 ∙ NCBI:171482 ∙ OMIM:300477 ∙ HGNC:18403 ∙ Uniprot:Q8IZU1 ∙ 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 FAM9A gene.

• not_specified (46 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM9A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000174951.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			44	3		47
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	4	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM9A	protein_coding	protein_coding	ENST00000543214	8	10589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-12	0.00607	125730	12	6	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.752	145	122	1.19	0.00000982	2182
Missense in Polyphen		25	19.951	1.2531		242
Synonymous	-0.288	46	43.6	1.06	0.00000375	577
Loss of Function	-1.29	15	10.5	1.43	6.63e-7	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000366	0.0000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000244	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000763	0.0000527
Middle Eastern	0.000244	0.000163
South Asian	0.000431	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.276
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.0639
• 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: 0.114

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;nucleolus
• Molecular function: protein binding