FRMD1

FERM domain containing 1, the group of FERM domain containing

Basic information

Region (hg38): 6:168053095-168101511

Links

ENSG00000153303 ∙ NCBI:79981 ∙ ∙ HGNC:21240 ∙ Uniprot:Q8N878 ∙ 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 FRMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMD1 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				5		5
missense			52	5	3	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	52	10	3

Variants in FRMD1

This is a list of pathogenic ClinVar variants found in the FRMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-168057122-G-T		not specified	Likely benign (Nov 09, 2022)
6-168057250-C-T			Likely benign (Dec 01, 2023)
6-168057264-C-A		not specified	Uncertain significance (Dec 27, 2023)
6-168057264-C-G		not specified	Uncertain significance (Nov 29, 2021)
6-168057275-A-T		not specified	Uncertain significance (Dec 14, 2022)
6-168059132-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-168059153-T-C		not specified	Uncertain significance (Aug 02, 2023)
6-168059182-C-T		not specified	Uncertain significance (Jan 24, 2023)
6-168060769-T-C		not specified	Uncertain significance (Dec 26, 2023)
6-168060776-G-A		not specified	Likely benign (Oct 12, 2022)
6-168060793-C-T		not specified	Uncertain significance (May 14, 2024)
6-168060805-G-C		not specified	Uncertain significance (Mar 07, 2024)
6-168060836-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-168060855-G-T		not specified	Uncertain significance (May 15, 2024)
6-168060860-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-168060876-T-A		not specified	Uncertain significance (Aug 08, 2022)
6-168060897-C-A		not specified	Uncertain significance (Sep 22, 2023)
6-168060944-G-A		not specified	Uncertain significance (Jun 26, 2023)
6-168060950-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-168060954-G-T			Benign (Nov 27, 2018)
6-168060997-C-G		not specified	Uncertain significance (Dec 14, 2022)
6-168061000-C-G		not specified	Uncertain significance (Jan 04, 2024)
6-168061043-G-A		not specified	Uncertain significance (Jan 09, 2024)
6-168061821-C-G		not specified	Uncertain significance (Aug 02, 2021)
6-168061848-C-T		not specified	Likely benign (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMD1	protein_coding	protein_coding	ENST00000283309	11	25813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.67e-14	0.0432	125594	0	150	125744	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0887	348	343	1.01	0.0000225	3524
Missense in Polyphen		107	97.938	1.0925		1081
Synonymous	-1.07	165	148	1.11	0.0000104	1074
Loss of Function	0.422	22	24.2	0.907	0.00000120	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00102
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000276	0.000272
Finnish	0.00199	0.00199
European (Non-Finnish)	0.000531	0.000528
Middle Eastern	0.000276	0.000272
South Asian	0.000363	0.000359
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.312
• rvis_EVS: 1.12
• rvis_percentile_EVS: 92.1

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.170
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoskeleton