Is CCDC112 p.Asp445Val (c.1334A>T) pathogenic?

CCDC112 p.Asp445Val (c.1334A>T) is classified Uncertain significance in CCDC112 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-27). AlphaMissense: likely pathogenic (0.8949); Very rare (popmax 0.00282%, afr).

How common is CCDC112 p.Asp445Val (c.1334A>T) in the general population?

CCDC112 p.Asp445Val (c.1334A>T) is very rare (popmax 0.00282%, afr) (gnomAD).

What do computational predictors say about CCDC112 p.Asp445Val (c.1334A>T)?

AlphaMissense predicts likely pathogenic (score 0.8949) — an in-silico prediction, not a clinical call.

CCDC112 p.Asp445Val

c.1334A>T · VCV3485899

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8949 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00282%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8949	likely pathogenic · top 3% in CCDC112
REVEL	0.28	benign-leaning
SaProt	LLR -5.14	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 1.8, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 29 kb · p 0.025 · regional, not allelic
Overall
CADD	29.0	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 D362V vs ClinVar D445V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00282% African / African-American · 2/70,862 alleles

Filtering AF 0.000468% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000175%

Overall 0.000289% 4/1,385,538 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00282%	35,431
Finnishnot grpmax-eligible	0.00178%	56,202
European (non-Finnish)	8.73e-05%	1,146,035

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.Asp445Val
Coding: c.1334A>T
MANE Select: NM_001040440
Type: single nucleotide variant
Location: chr5:115269797 (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-asp445val (accessed [today's date]).

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