FAM149A

family with sequence similarity 149 member A

Basic information

Region (hg38): 4:186104419-186175337

Links

ENSG00000109794 ∙ NCBI:25854 ∙ ∙ HGNC:24527 ∙ Uniprot:A5PLN7 ∙ 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 FAM149A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM149A 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			41	13		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	41	13	0

Variants in FAM149A

This is a list of pathogenic ClinVar variants found in the FAM149A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-186151981-A-T		not specified	Uncertain significance (Dec 07, 2021)
4-186153667-C-G		not specified	Uncertain significance (May 25, 2022)
4-186153718-G-A		not specified	Likely benign (Dec 13, 2023)
4-186153734-C-T		not specified	Likely benign (Jan 31, 2023)
4-186153762-C-A		not specified	Uncertain significance (Nov 06, 2023)
4-186154557-C-T		not specified	Uncertain significance (Oct 26, 2022)
4-186154605-T-C		not specified	Uncertain significance (Sep 16, 2021)
4-186154632-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-186154634-G-C		not specified	Uncertain significance (Dec 01, 2022)
4-186156002-A-T		not specified	Uncertain significance (Nov 28, 2023)
4-186156035-C-A		not specified	Likely benign (Jul 25, 2023)
4-186156046-T-A			Likely benign (Dec 01, 2022)
4-186156050-G-A			Likely benign (Dec 01, 2022)
4-186156068-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-186156077-C-T		not specified	Uncertain significance (Aug 26, 2022)
4-186156079-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-186156124-G-A		not specified	Uncertain significance (Dec 04, 2023)
4-186156145-C-T		not specified	Uncertain significance (Jun 13, 2024)
4-186157591-A-G			Likely benign (Aug 01, 2023)
4-186157595-T-C		not specified	Uncertain significance (Jul 14, 2021)
4-186157639-G-A		not specified	Likely benign (Apr 26, 2023)
4-186157703-G-A		not specified	Likely benign (Dec 13, 2023)
4-186162869-T-G		not specified	Uncertain significance (Sep 22, 2023)
4-186162870-A-G		not specified	Uncertain significance (Mar 24, 2023)
4-186162917-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM149A	protein_coding	protein_coding	ENST00000227065	11	68249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000136	0.991	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.315	310	295	1.05	0.0000182	3074
Missense in Polyphen		68	70.264	0.96778		846
Synonymous	-0.920	138	125	1.10	0.00000880	1006
Loss of Function	2.34	12	24.5	0.489	0.00000127	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000631	0.000631
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000652	0.000653
South Asian	0.000494	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.927
• rvis_EVS: 3.12
• rvis_percentile_EVS: 99.27

Haploinsufficiency Scores

• pHI: 0.0955
• hipred: N
• hipred_score: 0.324
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam149a