Is CCDC13 p.Asp55Gly (c.164A>G) pathogenic?

CCDC13 p.Asp55Gly (c.164A>G) is classified Benign in CCDC13 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-02-01). AlphaMissense: likely benign (0.0682); Low-frequency (popmax 1.35%, nfe).

How common is CCDC13 p.Asp55Gly (c.164A>G) in the general population?

CCDC13 p.Asp55Gly (c.164A>G) is low-frequency (popmax 1.35%, nfe) (gnomAD).

What do computational predictors say about CCDC13 p.Asp55Gly (c.164A>G)?

AlphaMissense predicts likely benign (score 0.0682) — an in-silico prediction, not a clinical call.

CCDC13 p.Asp55Gly

c.164A>G · rs34234072 · VCV2653714

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0682 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.35%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0682	likely benign
REVEL	0.007	strongly benign-leaning
SaProt	LLR -5.94	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 0.59	GERP -0.86, phastCons 0.001
Regional constraint	o/e 0.94	unconstrained · MANE · 49 kb · p 0.094 · regional, not allelic
Overall
CADD	10.89	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 1.35% European (non-Finnish) · 15,899/1,180,024 alleles

Filtering AF 1.33% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.32%

Overall 1.13% 18,260/1,614,142 alleles · low-frequency

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.87%	53
European (non-Finnish)grpmax	1.35%	74
Remaining individualsnot grpmax-eligible	0.941%	106
Admixed American	0.518%	193
African / African-American	0.206%	484
Ashkenazi Jewishnot grpmax-eligible	0.122%	822
South Asian	0.0725%	1,380
Middle Eastern	0.0497%	2,013
East Asian	0.00446%	22,442

Finnish 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: CCDC13
Protein: p.Asp55Gly
Coding: c.164A>G
MANE Select: NM_144719
dbSNP: rs34234072
Type: single nucleotide variant
Location: chr3:42758182 (GRCh38)
Gene constraint: LOEUF 0.906 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.77
Residue 55: the 'disordered' region

Full CCDC13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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CCDC13 p.Ala129Thr Uncertain significance ★ ⚠ same type
CCDC13 p.Ala175Thr Uncertain significance ★ ⚠ same type
CCDC13 p.Ala187Thr Uncertain significance ★ ⚠ same type
CCDC13 p.Ala332Gly Uncertain significance ★ ⚠ same type
CCDC13 p.Ala3Val Uncertain significance ★ ⚠ same type
CCDC13 p.Ala517Val Uncertain significance ★ ⚠ same type
CCDC13 p.Ala544Thr 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/ccdc13-p-asp55gly (accessed [today's date]).

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