Is CCDC136 p.Ser1009= (c.3027C>T) pathogenic?

CCDC136 p.Ser1009= (c.3027C>T) is classified Likely benign in CCDC136 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-01). Rare (popmax 0.372%, amr).

How common is CCDC136 p.Ser1009= (c.3027C>T) in the general population?

CCDC136 p.Ser1009= (c.3027C>T) is rare (popmax 0.372%, amr) (gnomAD).

CCDC136 p.Ser1009=

c.3027C>T · rs184775299 · VCV2657990

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.372%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.036	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.41
Overall
CADD	3.593	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.372% Admixed American · 215/57,792 alleles

Filtering AF 0.331% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.315%

Overall 0.0769% 1,226/1,594,982 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	1.1%	91
Admixed Americangrpmax	0.372%	269
African / African-American	0.267%	374
Remaining individualsnot grpmax-eligible	0.136%	736
Middle Eastern	0.133%	751
European (non-Finnish)	0.0589%	1,697
South Asian	0.0171%	5,851
Ashkenazi Jewishnot grpmax-eligible	0.0138%	7,267
East Asian	0.00451%	22,193

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CCDC136
Protein: p.Ser1009=
Coding: c.3027C>T
MANE Select: NM_022742
dbSNP: rs184775299
Type: single nucleotide variant
Location: chr7:128814901 (GRCh38)
Gene constraint: LOEUF 0.924 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.24

Full CCDC136 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC136 p.Ser1009Arg Uncertain significance ★ ⚠ same residue
CCDC136 p.Ala687= Benign ★★ same type
CCDC136 p.Asp218His Benign ★★ same type
CCDC136 p.Glu1087= Benign ★★ same type
CCDC136 p.Glu1097Gly Likely benign ★★ same type
CCDC136 p.Gly221= Benign ★★ same type
CCDC136 p.Gly980Arg Benign ★★ same type
CCDC136 p.Leu616= Benign ★★ 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/ccdc136-p-ser1009 (accessed [today's date]).

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