DNHD1 p.Ser4556=
c.13668G>C · VCV4681998
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.088 | GERP -2.9, phastCons 0.049 |
| Overall | ||
| CADD | 4.958 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DNHD1
- Protein
- p.Ser4556=
- Coding
- c.13668G>C
- MANE Select
- NM_144666
- Type
- single nucleotide variant
- Location
- chr11:6571180 (GRCh38)
- Gene constraint
- LOEUF 0.897 · pLI <0.01 (gnomAD)
- Residue 4556
- a UniProt-annotated variant site (in spgf65); a UniProt-annotated variant site (in spgf65; low expression, if any, in sperm flagella)
Similar variants
- DNHD1 p.Ser4556Leu Uncertain significance ★ ⚠ same residue
- DNHD1 p.Arg2928Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg3978Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg4048Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Glu1153Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Tyr2166Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg1582Trp Uncertain significance ★★ same type
- DNHD1 p.Arg1873Ser Uncertain significance ★★ same type
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/dnhd1-p-ser4556 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown