Is PSPH p.Arg134Ser (c.402G>T) pathogenic?

PSPH p.Arg134Ser (c.402G>T) is classified Uncertain significance in PSPH (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-17). AlphaMissense: likely pathogenic (0.729); Absent from gnomAD v4.1; Associated with PSPH deficiency.

What condition is associated with PSPH p.Arg134Ser (c.402G>T)?

PSPH p.Arg134Ser (c.402G>T) is associated with PSPH deficiency (ClinVar).

How common is PSPH p.Arg134Ser (c.402G>T) in the general population?

PSPH p.Arg134Ser (c.402G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PSPH p.Arg134Ser (c.402G>T)?

AlphaMissense predicts likely pathogenic (score 0.729) — an in-silico prediction, not a clinical call.

PSPH p.Arg134Ser

c.402G>T · rs2534871142 · VCV1994878

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.729 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

PSPH deficiency

Computational evidence

Protein change
AlphaMissense	0.729	likely pathogenic
REVEL	0.436	indeterminate
SaProt	LLR -4.17	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.76	GERP 1.6, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 9,447 bp · p 0.0022 · regional, not allelic
Overall
CADD	23.8	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PSPH
Protein: p.Arg134Ser
Coding: c.402G>T
MANE Select: NM_004577
dbSNP: rs2534871142
Type: single nucleotide variant
Location: chr7:56017253 (GRCh38)
Gene constraint: LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.88 · 6 PDB

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

Disease context

PSPH deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PSPH p.Arg101Ter Likely pathogenic ★★ same condition
PSPH c.422-3A>C Uncertain significance ★★ same condition
PSPH c.570+3A>G Uncertain significance ★★ same condition
PSPH c.570+5G>C Uncertain significance ★★ same condition
PSPH c.*341G>A Uncertain significance ★★ same condition
PSPH p.Asn124Ser Uncertain significance ★★ ⚠ same condition
PSPH p.Asp32Asn Uncertain significance ★★ ⚠ same condition
PSPH p.Gln204His Uncertain significance ★★ ⚠ same condition

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/psph-p-arg134ser (accessed [today's date]).

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