Is DNHD1 p.Ser986= (c.2958C>T) pathogenic?

DNHD1 p.Ser986= (c.2958C>T) is classified Likely benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-01). Rare (popmax 0.551%, mid); Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Ser986= (c.2958C>T)?

DNHD1 p.Ser986= (c.2958C>T) is associated with DNHD1-related disorder (ClinVar).

How common is DNHD1 p.Ser986= (c.2958C>T) in the general population?

DNHD1 p.Ser986= (c.2958C>T) is rare (popmax 0.551%, mid) (gnomAD).

DNHD1 p.Ser986=

c.2958C>T · rs555478816 · VCV3042736

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.551%, mid)

Conditions

DNHD1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.83	GERP -2.8
Overall
CADD	8.223	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.551% Middle Eastern · 33/5,990 alleles

Filtering AF 0.403% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.353%

Overall 0.00548% 85/1,551,244 alleles · rare exomes 78/1,399,184 · genomes 7/152,060 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.551%	182
Remaining individualsnot grpmax-eligible	0.015%	6,679
African / African-American	0.011%	9,132
Admixed American	0.00784%	12,747
East Asian	0.00489%	20,439
South Asian	0.00476%	21,010
European (non-Finnish)	0.00209%	47,786
Finnishnot grpmax-eligible	0.00167%	59,754

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: DNHD1
Protein: p.Ser986=
Coding: c.2958C>T
MANE Select: NM_144666
dbSNP: rs555478816
Type: single nucleotide variant
Location: chr11:6534133 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)

Full DNHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNHD1-related disorder

Similar variants

DNHD1 p.Ser986Thr Uncertain significance ★ ⚠ same residue
DNHD1 p.Glu4486Lys Uncertain significance ★★ ⚠ same condition
DNHD1 p.His4162Leu Uncertain significance ★★ ⚠ same condition
DNHD1 p.Arg2840Gln Uncertain significance ★ ⚠ same condition
DNHD1 p.Gln895Ter Conflicting classifications of pathogenicity ★ same condition
DNHD1 p.His3335Arg Uncertain significance ★ ⚠ same condition
DNHD1 p.Ala657Ser Uncertain significance ⚠ same condition
DNHD1 p.Glu971Lys Uncertain significance 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/dnhd1-p-ser986 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown