FAM9C

family with sequence similarity 9 member C

Basic information

Region (hg38): X:13035616-13044682

Links

ENSG00000187268 ∙ NCBI:171484 ∙ OMIM:300479 ∙ HGNC:18405 ∙ Uniprot:Q8IZT9 ∙ 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 FAM9C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM9C 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						0
missense			9			9
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	9	1	0

Variants in FAM9C

This is a list of pathogenic ClinVar variants found in the FAM9C 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-13038454-G-C		not specified	Uncertain significance (Apr 24, 2024)
X-13038476-A-C		not specified	Uncertain significance (Sep 29, 2022)
X-13039909-G-A		not specified	Uncertain significance (May 30, 2024)
X-13040782-A-G		not specified	Uncertain significance (Jun 30, 2022)
X-13040783-C-T		not specified	Uncertain significance (May 18, 2022)
X-13040870-C-T		not specified	Uncertain significance (Nov 18, 2023)
X-13042926-T-C		not specified	Uncertain significance (Jan 04, 2024)
X-13042959-A-G		not specified	Likely benign (Jun 23, 2016)
X-13043129-C-A		not specified	Uncertain significance (Jan 02, 2024)
X-13043165-C-T		not specified	Uncertain significance (Apr 04, 2023)
X-13043219-C-T		not specified	Uncertain significance (Jul 14, 2023)
X-13043755-A-T		not specified	Uncertain significance (Mar 31, 2024)
X-13043759-C-T		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM9C	protein_coding	protein_coding	ENST00000333995	6	9065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.88e-7	0.0693	121764	32	19	121815	0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.159	51	54.3	0.939	0.00000386	1109
Missense in Polyphen		6	7.9187	0.7577		203
Synonymous	-0.553	20	17.1	1.17	0.00000122	263
Loss of Function	-1.19	8	5.10	1.57	3.20e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000157	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000771	0.0000539
Middle Eastern	0.000157	0.000111
South Asian	0.00286	0.00153
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.767
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.00768
• hipred: N
• hipred_score: 0.112
• ghis: 0.433

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
• Molecular function: protein binding