Is DCBLD1 p.Ala15Ser (c.43G>T) pathogenic?

DCBLD1 p.Ala15Ser (c.43G>T) is classified Uncertain significance in DCBLD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-01). AlphaMissense: likely benign (0.1748); Very rare (popmax 0.0094%, nfe).

How common is DCBLD1 p.Ala15Ser (c.43G>T) in the general population?

DCBLD1 p.Ala15Ser (c.43G>T) is very rare (popmax 0.0094%, nfe) (gnomAD).

What do computational predictors say about DCBLD1 p.Ala15Ser (c.43G>T)?

AlphaMissense predicts likely benign (score 0.1748) — an in-silico prediction, not a clinical call.

DCBLD1 p.Ala15Ser

c.43G>T · rs1051771967 · VCV3080374

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1748 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0094%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1748	likely benign
REVEL	0.15	moderately benign-leaning
SaProt	LLR -8.04	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 0.76	GERP -1.3
Regional constraint	o/e 0.96	unconstrained · MANE · 66 kb · p 0.29 · regional, not allelic
Overall
CADD	8.452	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0094% European (non-Finnish) · 89/946,746 alleles

Filtering AF 0.00776% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00715%

Overall 0.00798% 93/1,165,856 alleles · very rare exomes 80/1,015,200 · genomes 13/150,656 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0094%	10,638
Remaining individualsnot grpmax-eligible	0.00738%	13,543
Finnishnot grpmax-eligible	0.0036%	27,780

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: DCBLD1
Protein: p.Ala15Ser
Coding: c.43G>T
MANE Select: NM_001366458
dbSNP: rs1051771967
Type: single nucleotide variant
Location: chr6:117482824 (GRCh38)
Gene constraint: LOEUF 0.942 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.00

Full DCBLD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCBLD1 p.Asp151Asn Uncertain significance ★★ ⚠ same type
DCBLD1 p.Ala182Val Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala206Thr Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala28Val Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala479Asp Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala509Ser Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala5Gly Uncertain significance ★ ⚠ same type
DCBLD1 p.Ala95Val 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/dcbld1-p-ala15ser (accessed [today's date]).

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