FAM172A

family with sequence similarity 172 member A, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:93617724-94111699

Previous symbols: [ "C5orf21" ]

Links

ENSG00000113391 ∙ NCBI:83989 ∙ ∙ HGNC:25365 ∙ Uniprot:Q8WUF8 ∙ 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 FAM172A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM172A 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			12			12
Total	0	0	31	0	0

Variants in FAM172A

This is a list of pathogenic ClinVar variants found in the FAM172A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-93620998-C-G		not specified	Uncertain significance (Jun 26, 2024)
5-93621079-T-G		not specified	Uncertain significance (Mar 08, 2024)
5-93740605-G-A		not specified	Uncertain significance (May 27, 2022)
5-93740656-G-C		not specified	Uncertain significance (Apr 25, 2023)
5-93740710-C-A		not specified	Likely benign (Mar 31, 2024)
5-93740905-C-G		not specified	Uncertain significance (Apr 27, 2023)
5-93740905-C-T		not specified	Uncertain significance (Oct 17, 2023)
5-93740908-C-T		not specified	Uncertain significance (Sep 24, 2024)
5-93740986-G-A		not specified	Uncertain significance (Dec 06, 2023)
5-93741026-G-C		not specified	Uncertain significance (Apr 09, 2024)
5-93741086-T-G		not specified	Uncertain significance (Jun 02, 2024)
5-93741107-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-93741139-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-93741241-C-G		not specified	Uncertain significance (Dec 28, 2023)
5-93741269-C-A		not specified	Uncertain significance (Nov 19, 2022)
5-93741284-G-A		not specified	Uncertain significance (Nov 05, 2021)
5-93741530-G-T		not specified	Uncertain significance (May 18, 2022)
5-93741540-G-C		not specified	Uncertain significance (Jul 09, 2024)
5-93784405-G-A		not specified	Uncertain significance (Sep 24, 2024)
5-93784441-G-C		not specified	Uncertain significance (Nov 23, 2024)
5-93784489-C-T		not specified	Uncertain significance (Jul 12, 2023)
5-93824186-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-93824206-G-A		not specified	Uncertain significance (Feb 15, 2023)
5-93824219-T-C		not specified	Uncertain significance (Jun 09, 2022)
5-93824257-G-A		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM172A	protein_coding	protein_coding	ENST00000395965	10	493630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000244	0.996	125712	0	27	125739	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.365	208	223	0.931	0.0000114	2738
Missense in Polyphen		63	68.57	0.91876		850
Synonymous	-0.0619	81	80.3	1.01	0.00000431	749
Loss of Function	2.57	10	23.4	0.427	0.00000124	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of alternative splicing, by interacting with AGO2 and CHD7. Seems to be required for stabilizing protein-protein interactions at the chromatin- spliceosome interface. May have hydrolase activity. {ECO:0000250|UniProtKB:Q3TNH5}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.340
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.372
• hipred: N
• hipred_score: 0.492
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam172a

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;RNA splicing;neural crest cell development;chromatin silencing by small RNA
• Cellular component: nucleus;endoplasmic reticulum
• Molecular function: siRNA binding