Is DCDC1 p.Ser1701Pro (c.5101T>C) pathogenic?

DCDC1 p.Ser1701Pro (c.5101T>C) is classified Benign in DCDC1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-05-08). AlphaMissense: ambiguous (0.4492); Low-frequency (popmax 3.6%, afr).

How common is DCDC1 p.Ser1701Pro (c.5101T>C) in the general population?

DCDC1 p.Ser1701Pro (c.5101T>C) is low-frequency (popmax 3.6%, afr) (gnomAD).

What do computational predictors say about DCDC1 p.Ser1701Pro (c.5101T>C)?

AlphaMissense predicts ambiguous (score 0.4492) — an in-silico prediction, not a clinical call.

DCDC1 p.Ser1701Pro

c.5101T>C · rs55719241 · VCV718774

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.4492 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.6%, afr)

Computational evidence

Protein change
AlphaMissense	0.4492	ambiguous
SaProt	LLR -10.56	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -0.62
Regional constraint	o/e 1.13	unconstrained · MANE · 450 kb · p 2.3e-08 · regional, not allelic
Overall
CADD	21.2	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 S1698P vs ClinVar S1701P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.6% African / African-American · 2,699/74,980 alleles

Filtering AF 3.49% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.44%

Overall 0.202% 3,254/1,613,262 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.6%	28
Middle Eastern	0.298%	336
Remaining individualsnot grpmax-eligible	0.269%	372
Admixed American	0.233%	428
European (non-Finnish)	0.0184%	5,435
South Asian	0.011%	9,107
Finnishnot grpmax-eligible	0.00312%	32,004

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: DCDC1
Protein: p.Ser1701Pro
Coding: c.5101T>C
MANE Select: NM_001387274
dbSNP: rs55719241
Type: single nucleotide variant
Location: chr11:30881290 (GRCh38)
Gene constraint: LOEUF 1.093 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.53

Full DCDC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCDC1 p.Gln95His Uncertain significance ★★ ⚠ same type
DCDC1 p.Thr239Met Uncertain significance ★★ ⚠ same type
DCDC1 p.Thr317Ala Uncertain significance ★★ ⚠ same type
DCDC1 c.591+13C>T Benign ★★ same type
DCDC1 p.Ala1431Thr Benign ★★ ⚠ same type
DCDC1 p.Glu200= Benign ★★ same type
DCDC1 p.Leu224= Benign ★★ same type
DCDC1 p.Lys1494Arg 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/dcdc1-p-ser1701pro (accessed [today's date]).

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