Is DRC4 p.Ser136Thr (c.407G>C) pathogenic?

DRC4 p.Ser136Thr (c.407G>C) is classified Benign/Likely benign in DRC4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-24). AlphaMissense: likely benign (0.0713); Low-frequency (popmax 1.55%, eas); Associated with primary ciliary dyskinesia 33.

What condition is associated with DRC4 p.Ser136Thr (c.407G>C)?

DRC4 p.Ser136Thr (c.407G>C) is associated with primary ciliary dyskinesia 33 (ClinVar).

How common is DRC4 p.Ser136Thr (c.407G>C) in the general population?

DRC4 p.Ser136Thr (c.407G>C) is low-frequency (popmax 1.55%, eas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DRC4 p.Ser136Thr (c.407G>C)?

AlphaMissense predicts likely benign (score 0.0713) — an in-silico prediction, not a clinical call.

DRC4 p.Ser136Thr

c.407G>C · rs148760410 · VCV542271

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0713 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.55%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia 33

Computational evidence

Protein change
AlphaMissense	0.0713	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -6.49	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.2	phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 21 kb · p 0.0024 · regional, not allelic
Overall
CADD	9.779	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.55% East Asian · 695/44,888 alleles

Filtering AF 1.45% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.41%

Overall 0.0768% 1,239/1,613,970 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.55%	65
Remaining individualsnot grpmax-eligible	0.29%	345
Admixed American	0.0367%	2,727
South Asian	0.0351%	2,846
Ashkenazi Jewishnot grpmax-eligible	0.0338%	2,960
Finnishnot grpmax-eligible	0.0328%	3,049
European (non-Finnish)	0.0235%	4,260
African / African-American	0.00133%	74,958

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: DRC4
Protein: p.Ser136Thr
Coding: c.407G>C
MANE Select: NM_001481
dbSNP: rs148760410
Type: single nucleotide variant
Location: chr16:90032836 (GRCh38)
Structure: AlphaFold pLDDT 85.12 · 1 PDB
Residue 136: the 'microtubule-binding' region

Full DRC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DRC4 c.495+1G>T Likely pathogenic ★★ same condition
DRC4 p.Gln357Ter Pathogenic ★★ same condition
DRC4 p.Ala280Thr Uncertain significance ★★ ⚠ same condition
DRC4 p.Ala460Pro Uncertain significance ★★ ⚠ same condition
DRC4 p.Arg143Trp Uncertain significance ★★ ⚠ same condition
DRC4 p.Arg164Trp Uncertain significance ★★ ⚠ same condition
DRC4 p.Arg203Gln Uncertain significance ★★ ⚠ same condition
DRC4 p.Arg278Cys 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/drc4-p-ser136thr (accessed [today's date]).

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