DYNC2H1 p.Arg3622=
c.10864C>A · rs117178504 · VCV220090
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, nfe)
Conditions
2
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 4.6 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 5.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
European (non-Finnish) · 15,048/1,176,088 alleles
Filtering AF
1.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
1.06%
17,039/1,607,294 alleles · low-frequency
exomes 15,878/1,455,232 · genomes 1,161/152,062 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 1.09% | 92 |
| Admixed American | 1.03% | 97 |
| Ashkenazi Jewishnot grpmax-eligible | 0.996% | 100 |
| Middle Eastern | 0.364% | 275 |
| Finnishnot grpmax-eligible | 0.275% | 364 |
| African / African-American | 0.227% | 440 |
| South Asian | 0.0468% | 2,136 |
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.Arg3622=
- Coding
- c.10864C>A
- MANE Select
- NM_001377
- dbSNP
- rs117178504
- Type
- single nucleotide variant
- Location
- chr11:103283059 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3622
- an α-helix
Similar variants
- DYNC2H1 p.Arg3622Ter Pathogenic/Likely pathogenic ★★ same residue
- DYNC2H1 p.Arg3622Pro 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
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-arg3622 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown