FAM86C1P

family with sequence similarity 86 member C1, pseudogene

Basic information

Region (hg38): 11:71787537-71799660

Previous symbols: [ "FAM86C", "FAM86C1" ]

Links

ENSG00000158483 ∙ NCBI:55199 ∙ OMIM:616124 ∙ HGNC:25561 ∙ Uniprot:Q9NVL1 ∙ 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 FAM86C1P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM86C1P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding			17	2		19
Total	0	0	17	2	0

Variants in FAM86C1P

This is a list of pathogenic ClinVar variants found in the FAM86C1P region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-71787555-G-A		not specified	Uncertain significance (Jan 15, 2025)
11-71787569-C-A			Likely benign (Oct 01, 2024)
11-71787609-G-A		not specified	Uncertain significance (May 24, 2023)
11-71789829-G-A		not specified	Uncertain significance (Aug 12, 2024)
11-71793380-C-T		not specified	Uncertain significance (Oct 03, 2024)
11-71793467-C-T		not specified	Uncertain significance (Jul 30, 2024)
11-71796024-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-71796047-C-T		not specified	Uncertain significance (Feb 25, 2025)
11-71796054-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-71796065-G-A		not specified	Likely benign (Dec 21, 2022)
11-71796083-G-T		not specified	Uncertain significance (Dec 17, 2024)
11-71796087-G-T		not specified	Uncertain significance (Feb 19, 2025)
11-71796098-C-A		not specified	Uncertain significance (Mar 14, 2025)
11-71796123-C-A		not specified	Uncertain significance (Mar 29, 2023)
11-71796123-C-T		not specified	Uncertain significance (Feb 22, 2023)
11-71796138-G-A		not specified	Uncertain significance (Mar 18, 2024)
11-71796158-C-A		not specified	Uncertain significance (May 03, 2023)
11-71796161-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-71796164-T-C		not specified	Uncertain significance (Jan 01, 2025)
11-71796165-A-G		not specified	Uncertain significance (Jun 05, 2023)
11-71799562-C-T		not specified	Uncertain significance (Mar 01, 2025)
11-71799576-G-T		not specified	Uncertain significance (Nov 15, 2024)
11-71799589-A-G		not specified	Uncertain significance (Jan 08, 2025)
11-71799631-G-T		not specified	Uncertain significance (Dec 06, 2024)
11-71799636-T-C		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM86C1P	protein_coding	protein_coding	ENST00000359244	5	13727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.56e-12	0.00445	125532	0	39	125571	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.69	133	88.4	1.50	0.00000512	1010
Missense in Polyphen		35	25.208	1.3885		337
Synonymous	-2.87	58	36.1	1.61	0.00000213	310
Loss of Function	-1.76	14	8.47	1.65	3.61e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000579	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000548	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000169	0.000168
Middle Eastern	0.000548	0.000544
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: N
• hipred_score: 0.148
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: methylation
• Cellular component: protein-containing complex
• Molecular function: protein binding;methyltransferase activity