Is DDHD1 p.Ser114= (c.342C>T) pathogenic?

DDHD1 p.Ser114= (c.342C>T) is classified Likely benign in DDHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-01-12). Very rare (popmax 0.00308%, afr); Associated with DDHD1-related disorder.

What condition is associated with DDHD1 p.Ser114= (c.342C>T)?

DDHD1 p.Ser114= (c.342C>T) is associated with DDHD1-related disorder (ClinVar).

How common is DDHD1 p.Ser114= (c.342C>T) in the general population?

DDHD1 p.Ser114= (c.342C>T) is very rare (popmax 0.00308%, afr) (gnomAD).

DDHD1 p.Ser114=

c.342C>T · rs777615996 · VCV3036848

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00308%, afr)

Conditions

DDHD1-related disorder

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 0.005	GERP 0.38
Overall
CADD	9.924	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00308% African / African-American · 2/64,992 alleles

Filtering AF 0.00203% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00174%

Overall 0.00222% 34/1,529,676 alleles · very rare exomes 32/1,444,228 · genomes 2/85,448 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00308%	32,496
European (non-Finnish)	0.00281%	35,599

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: DDHD1
Protein: p.Ser114=
Coding: c.342C>T
MANE Select: NM_001160148
dbSNP: rs777615996
Type: single nucleotide variant
Location: chr14:53152757 (GRCh38)
Gene constraint: LOEUF 0.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 67.11
Residue 114: the 'disordered' region

Full DDHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DDHD1-related disorder

Similar variants

DDHD1 p.Ser114Phe Uncertain significance ★★ ⚠ same residue
DDHD1 p.Ser114Pro Uncertain significance ★★ ⚠ same residue
DDHD1 p.Ala193Val Uncertain significance ★★ ⚠ same type
DDHD1 p.Ala94Pro Uncertain significance ★★ ⚠ same type
DDHD1 p.Arg204Trp Uncertain significance ★★ ⚠ same type
DDHD1 p.Arg288His Uncertain significance ★★ ⚠ same type
DDHD1 p.Arg554Gln Uncertain significance ★★ ⚠ same type
DDHD1 p.Arg570Gln 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/ddhd1-p-ser114 (accessed [today's date]).

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