DYNC2H1 p.Val4014=
c.12042T>C · rs199929555 · VCV1610837
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0598%, afr)
Conditions
1
Jeune syndrome
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 0.033 | GERP -2.3, phastCons 0.96 |
| Overall | ||
| CADD | 2.801 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0598%
African / African-American · 44/73,630 alleles
Filtering AF
0.0457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0408%
Overall
0.00336%
52/1,546,534 alleles · ultra-rare
exomes 23/1,394,194 · genomes 29/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0598% | 1,673 |
| Remaining individualsnot grpmax-eligible | 0.00999% | 10,008 |
| Admixed American | 0.00189% | 52,990 |
| South Asian | 0.0012% | 83,012 |
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
- DYNC2H1
- Protein
- p.Val4014=
- Coding
- c.12042T>C
- MANE Select
- NM_001377
- dbSNP
- rs199929555
- Type
- single nucleotide variant
- Location
- chr11:103358245 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 4014
- an α-helix
Similar variants
- DYNC2H1 p.Val4014Ile Uncertain significance ★★ ⚠ same residue
- DYNC2H1 c.10042+2T>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10462-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.10606-14A>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10695+1G>A Likely pathogenic ★★ same condition
- DYNC2H1 c.10813-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.11493+2T>A Likely pathogenic ★★ same condition
- DYNC2H1 c.11650-1G>A Pathogenic/Likely 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/dync2h1-p-val4014 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown