FAM72D

family with sequence similarity 72 member D

Basic information

Region (hg38): 1:145095974-145112696

Links

ENSG00000215784 ∙ NCBI:728833 ∙ OMIM:614712 ∙ HGNC:33593 ∙ Uniprot:Q6L9T8 ∙ 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 FAM72D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM72D 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in FAM72D

This is a list of pathogenic ClinVar variants found in the FAM72D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145096920-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-145096983-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-145099014-A-G		not specified	Uncertain significance (Oct 20, 2021)
1-145099049-A-G		not specified	Uncertain significance (Apr 27, 2023)
1-145103079-C-A		not specified	Uncertain significance (Aug 12, 2021)
1-145103114-A-G		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM72D	protein_coding	protein_coding	ENST00000400889	4	16692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0299	0.609	124611	0	6	124617	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.687	23	34.3	0.670	0.00000146	975
Missense in Polyphen		11	16.528	0.66555		358
Synonymous	1.02	7	11.4	0.616	4.94e-7	263
Loss of Function	0.189	2	2.31	0.866	9.73e-8	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000135	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.00000892	0.00000885
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytosol;membrane;intracellular membrane-bounded organelle