DNAH1 p.Ser618=
c.1854A>C · rs374578700 · VCV787715
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.354%, sas)
Conditions
2
spermatogenic failure 18
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -2.6 |
| Overall | ||
| CADD | 0.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.354%
South Asian · 322/91,082 alleles
Filtering AF
0.322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.309%
Overall
0.0209%
338/1,614,054 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.354% | 283 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,464 |
| African / African-American | 0.00133% | 75,066 |
| European (non-Finnish) | 8.48e-05% | 1,179,898 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DNAH1
- Protein
- p.Ser618=
- Coding
- c.1854A>C
- MANE Select
- NM_015512
- dbSNP
- rs374578700
- Type
- single nucleotide variant
- Location
- chr3:52346669 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Residue 618
- the 'stem' region
Similar variants
- DNAH1 c.1034-2A>G Likely pathogenic ★★ same condition
- DNAH1 c.10474+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DNAH1 c.10968+2C>T Likely pathogenic ★★ same condition
- DNAH1 c.5244+1G>A Likely pathogenic ★★ same condition
- DNAH1 p.Arg1702Ter Pathogenic ★★ same condition
- DNAH1 p.Arg2479Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAH1 p.Arg2622Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAH1 p.Arg2724Ter Pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dnah1-p-ser618 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown