Is CCDC112 p.Gln317Arg (c.950A>G) pathogenic?

CCDC112 p.Gln317Arg (c.950A>G) is classified Benign in CCDC112 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-12-26). AlphaMissense: likely benign (0.0974); Rare (popmax 0.907%, afr).

How common is CCDC112 p.Gln317Arg (c.950A>G) in the general population?

CCDC112 p.Gln317Arg (c.950A>G) is rare (popmax 0.907%, afr) (gnomAD).

What do computational predictors say about CCDC112 p.Gln317Arg (c.950A>G)?

AlphaMissense predicts likely benign (score 0.0974) — an in-silico prediction, not a clinical call.

CCDC112 p.Gln317Arg

c.950A>G · rs77012548 · VCV711929

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0974 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.907%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0974	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -7.63	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 5	GERP 2, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 29 kb · p 0.025 · regional, not allelic
Overall
CADD	19.98	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM Q234R vs ClinVar Q317R) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.907% African / African-American · 645/71,120 alleles

Filtering AF 0.849% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.826%

Overall 0.0463% 716/1,547,874 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.907%	110
Admixed American	0.0739%	1,354
Remaining individualsnot grpmax-eligible	0.0589%	1,699
Middle Eastern	0.0347%	2,882
European (non-Finnish)	8.65e-05%	1,155,566

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: CCDC112
Protein: p.Gln317Arg
Coding: c.950A>G
MANE Select: NM_001040440
dbSNP: rs77012548
Type: single nucleotide variant
Location: chr5:115271595 (GRCh38)
Gene constraint: LOEUF 0.875 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.18

Full CCDC112 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC112 p.Ala165Val Uncertain significance ★ ⚠ same type
CCDC112 p.Ala299Ser Uncertain significance ★ ⚠ same type
CCDC112 p.Ala434Pro Uncertain significance ★ ⚠ same type
CCDC112 p.Ala68Pro Uncertain significance ★ same type
CCDC112 p.Arg391Cys Uncertain significance ★ ⚠ same type
CCDC112 p.Arg391His Uncertain significance ★ ⚠ same type
CCDC112 p.Arg391Leu Uncertain significance ★ ⚠ same type
CCDC112 p.Arg393Leu 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/ccdc112-p-gln317arg (accessed [today's date]).

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