FHDC1

FH2 domain containing 1, the group of Formins

Basic information

Region (hg38): 4:152936323-152979671

Links

ENSG00000137460 ∙ NCBI:85462 ∙ OMIM:620268 ∙ HGNC:29363 ∙ Uniprot:Q9C0D6 ∙ 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 FHDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FHDC1 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				2	4	6
missense			109	5	5	119
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	109	7	9

Variants in FHDC1

This is a list of pathogenic ClinVar variants found in the FHDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-152943181-C-G		not specified	Uncertain significance (Jun 16, 2024)
4-152943182-C-T		not specified	Uncertain significance (Mar 24, 2023)
4-152943259-G-A		not specified	Uncertain significance (Aug 02, 2023)
4-152943271-A-T		not specified	Uncertain significance (Apr 24, 2024)
4-152943307-C-T		not specified	Uncertain significance (Jun 13, 2022)
4-152943343-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-152943374-C-A		not specified	Uncertain significance (Jul 16, 2024)
4-152943415-G-A		not specified	Uncertain significance (Feb 22, 2025)
4-152953503-C-A		not specified	Uncertain significance (Oct 24, 2024)
4-152953521-G-A		not specified	Uncertain significance (Feb 21, 2024)
4-152954225-G-A		not specified	Likely benign (Nov 29, 2023)
4-152954230-A-T		not specified	Uncertain significance (Oct 17, 2024)
4-152954246-A-G		not specified	Uncertain significance (Jul 05, 2023)
4-152954269-G-A		not specified	Uncertain significance (Jul 13, 2022)
4-152954287-G-A		not specified	Uncertain significance (Jul 11, 2023)
4-152954318-A-C		not specified	Uncertain significance (Nov 07, 2024)
4-152960590-G-A		not specified	Uncertain significance (Apr 09, 2024)
4-152960595-G-A		not specified	Uncertain significance (Jul 05, 2023)
4-152960596-T-C		not specified	Uncertain significance (Sep 10, 2024)
4-152960746-A-G		not specified	Uncertain significance (Oct 27, 2022)
4-152960755-G-A		not specified	Uncertain significance (Dec 16, 2023)
4-152960794-C-T		not specified	Uncertain significance (Jul 14, 2023)
4-152962829-A-G		not specified	Uncertain significance (Jan 12, 2024)
4-152962834-C-A		not specified	Uncertain significance (Nov 26, 2024)
4-152963035-G-A		not specified	Uncertain significance (Nov 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FHDC1	protein_coding	protein_coding	ENST00000511601	11	43345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000634	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.110	659	667	0.988	0.0000397	7346
Missense in Polyphen		156	182.57	0.85447		2170
Synonymous	-0.0337	275	274	1.00	0.0000168	2392
Loss of Function	3.55	14	37.4	0.374	0.00000198	464

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000132
Middle Eastern	0.000221	0.000217
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated formin which regulates both actin and microtubule dynamics. Induces microtubule acetylation and stabilization and actin stress fiber formation (PubMed:18815276). Regulates Golgi ribbon formation (PubMed:26564798). Required for normal cilia assembly. Early in cilia assembly, may assist in the maturation and positioning of the centrosome/basal body, and once cilia assembly has initiated, may also promote cilia elongation by inhibiting disassembly (PubMed:29742020). {ECO:0000269|PubMed:18815276, ECO:0000269|PubMed:26564798, ECO:0000269|PubMed:29742020}.

Recessive Scores

• pRec: 0.0895

Intolerance Scores

• loftool: 0.662
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.21

Haploinsufficiency Scores

• pHI: 0.397
• hipred: N
• hipred_score: 0.313
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0778

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Fhdc1

Gene ontology

• Biological process: stress fiber assembly;cilium assembly;Golgi ribbon formation
• Cellular component: Golgi apparatus;microtubule;cytoplasmic microtubule;cilium
• Molecular function: actin binding;microtubule binding