FHAD1

protein-coding

forkhead associated phosphopeptide binding domain 1

Gene summary

Predicted to act upstream of or within apoptotic process and spermatogenesis. Located in sperm flagellum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001391957.1

Inheritance

—

ClinVar variants

U:207B:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr1:15,236,521-15,400,283

External References & Databases

Ensembl (ENSG00000142621)

Transcript & Mutation Effects

hg38 • Region Span ~163.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FHAD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 211

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001391957.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar		7
missense			197 clinvar	14 clinvar		211
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	207	17	0	224

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001391957.1	RefSeq	NP_001378886.1	33	MANE Select
ENST00000688493.1	Ensembl	ENSP00000509124.1	33	MANE Select
NM_052929.2	RefSeq	NP_443161.1	30	Standard
ENST00000314668.13	Ensembl	ENSP00000318812.9	14	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375995
Coding exons: 6
Length: 153012
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.996	97	129	0.753	0.00000720	1642
Missense (PolyPhen)		22	34.653	0.63487		471
Synonymous	1.54	43	58.0	0.742	0.00000365	462
Loss of Function	0.813	7	9.74	0.719	4.10e-7	140

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0584

Gene Damage Prediction

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