FAM171A1

family with sequence similarity 171 member A1

Basic information

Region (hg38): 10:15211643-15371289

Previous symbols: [ "C10orf38" ]

Links

ENSG00000148468 ∙ NCBI:221061 ∙ ∙ HGNC:23522 ∙ Uniprot:Q5VUB5 ∙ 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 FAM171A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM171A1 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			54			54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	0	0

Variants in FAM171A1

This is a list of pathogenic ClinVar variants found in the FAM171A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-15212997-T-A		not specified	Uncertain significance (Sep 25, 2023)
10-15213016-C-T		not specified	Uncertain significance (Dec 07, 2023)
10-15213019-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-15213064-C-T		not specified	Uncertain significance (Mar 20, 2024)
10-15213096-A-C		not specified	Uncertain significance (Aug 01, 2022)
10-15213157-T-C		not specified	Uncertain significance (Dec 06, 2022)
10-15213168-G-A		not specified	Uncertain significance (Oct 25, 2022)
10-15213171-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-15213175-C-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
10-15213184-C-T		not specified	Uncertain significance (Dec 18, 2023)
10-15213205-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-15213274-G-T		not specified	Uncertain significance (Dec 20, 2023)
10-15213289-G-A		not specified	Uncertain significance (Nov 03, 2022)
10-15213296-C-A		not specified	Uncertain significance (Mar 15, 2024)
10-15213322-T-A		not specified	Uncertain significance (Jun 17, 2024)
10-15213342-G-A		not specified	Uncertain significance (Oct 29, 2021)
10-15213415-T-C		not specified	Uncertain significance (May 04, 2023)
10-15213423-T-C		not specified	Uncertain significance (Jan 11, 2023)
10-15213450-T-C		not specified	Uncertain significance (Oct 16, 2023)
10-15213480-G-A		not specified	Uncertain significance (Mar 12, 2024)
10-15213498-C-G		not specified	Uncertain significance (Mar 20, 2023)
10-15213499-C-G		not specified	Uncertain significance (Jul 06, 2022)
10-15213561-G-A		not specified	Uncertain significance (Jun 16, 2024)
10-15213659-G-C		not specified	Uncertain significance (Jun 03, 2022)
10-15213684-G-A		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM171A1	protein_coding	protein_coding	ENST00000378116	8	159420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0147	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	511	540	0.947	0.0000346	5751
Missense in Polyphen		187	208.39	0.89735		2268
Synonymous	0.0965	251	253	0.992	0.0000193	1837
Loss of Function	4.68	5	34.8	0.144	0.00000190	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000590	0.0000590
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.268
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.73

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.699
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam171a1

Gene ontology

• Cellular component: integral component of membrane