FAM9A

family with sequence similarity 9 member A

Basic information

Region (hg38): X:8790794-8801383

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.

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.

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			15	1		16
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	2	1

Variants in FAM9A

This is a list of pathogenic ClinVar variants found in the FAM9A 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-8791359-G-T		not specified	Uncertain significance (Apr 09, 2022)
X-8791373-T-C		not specified	Uncertain significance (Apr 06, 2024)
X-8791374-G-A			Benign (Jun 27, 2018)
X-8793672-C-T		not specified	Uncertain significance (May 09, 2022)
X-8795123-TTC-T			Likely benign (Nov 01, 2022)
X-8795154-C-T		not specified	Uncertain significance (May 06, 2022)
X-8795269-C-T		not specified	Uncertain significance (Nov 08, 2022)
X-8795299-C-T		not specified	Uncertain significance (May 11, 2022)
X-8795413-G-A		not specified	Uncertain significance (Jan 05, 2022)
X-8795423-G-A			Benign (May 14, 2018)
X-8796278-G-T		not specified	Uncertain significance (Apr 13, 2023)
X-8798407-T-A		not specified	Uncertain significance (Jan 02, 2024)
X-8798414-C-T		not specified	Uncertain significance (Dec 20, 2023)
X-8798977-T-C			Likely benign (Dec 01, 2022)
X-8798983-G-A		not specified	Uncertain significance (Mar 18, 2024)
X-8798991-C-A		not specified	Uncertain significance (May 25, 2022)
X-8799050-G-A		not specified	Uncertain significance (Apr 14, 2023)
X-8799056-T-C		not specified	Uncertain significance (Mar 04, 2024)
X-8800093-C-A		not specified	Uncertain significance (Aug 26, 2022)
X-8800158-C-T		not specified	Uncertain significance (Oct 03, 2022)

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