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.

• not_specified (141 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_001010924.2. 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						0
missense			139	3		142
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	139	3	0

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